Package picard.analysis
Class CollectWgsMetrics.WgsMetricsCollector
- java.lang.Object
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- picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
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- picard.analysis.CollectWgsMetrics.WgsMetricsCollector
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- Direct Known Subclasses:
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- Enclosing class:
- CollectWgsMetrics
protected static class CollectWgsMetrics.WgsMetricsCollector extends AbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
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Field Summary
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Fields inherited from class picard.analysis.AbstractWgsMetricsCollector
counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray
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Constructor Summary
Constructors Constructor Description WgsMetricsCollector(CollectWgsMetrics metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN)
Accumulates the data from AbstractLocusInfo in inner structures-
Methods inherited from class picard.analysis.AbstractWgsMetricsCollector
addBaseQHistogram, addToMetricsFile, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounter
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Constructor Detail
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WgsMetricsCollector
public WgsMetricsCollector(CollectWgsMetrics metrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)
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Method Detail
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addInfo
public void addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN)
Description copied from class:AbstractWgsMetricsCollector
Accumulates the data from AbstractLocusInfo in inner structures- Specified by:
addInfo
in classAbstractWgsMetricsCollector<htsjdk.samtools.util.SamLocusIterator.RecordAndOffset>
- Parameters:
info
-AbstractLocusInfo
with aligned to reference position readsref
-ReferenceSequence
referenceBaseN
- true if current the value of reference base represents a no call
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